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NM_017446.4(MRPL39):c.896G>T (p.Gly299Val) AND Mitochondrial disease

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Feb 4, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002051599.3

Allele description [Variation Report for NM_017446.4(MRPL39):c.896G>T (p.Gly299Val)]

NM_017446.4(MRPL39):c.896G>T (p.Gly299Val)

Gene:
MRPL39:mitochondrial ribosomal protein L39 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q21.3
Genomic location:
Preferred name:
NM_017446.4(MRPL39):c.896G>T (p.Gly299Val)
HGVS:
  • NC_000021.9:g.25592837C>A
  • NM_017446.4:c.896G>TMANE SELECT
  • NM_080794.4:c.896G>T
  • NP_059142.3:p.Gly299Val
  • NP_542984.3:p.Gly299Val
  • NC_000021.8:g.26965149C>A
Protein change:
G299V; GLY299VAL
Links:
OMIM: 611845.0004; dbSNP: rs1227035820
NCBI 1000 Genomes Browser:
rs1227035820
Molecular consequence:
  • NM_017446.4:c.896G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080794.4:c.896G>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Mitochondrial disease
Synonyms:
Mitochondrial diseases; Mitochondrial disorder
Identifiers:
MONDO: MONDO:0044970; MeSH: D028361; MedGen: C0751651; Orphanet: 68380

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002107493Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet
no assertion criteria provided
Likely pathogenic
(Mar 24, 2022) 		biparentalclinical testing

SCV004801526Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Likely pathogenic
(Feb 4, 2021) 		unknownclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
Caucasianbiparentalyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, SCV002107493.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasian1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1biparentalyesnot providednot providednot provided1not providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV004801526.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The MRPL39 c.896G>T p.(Gly299Val) variant has been identified in a homozygous state in individuals with a phenotype consistent with primary mitochondrial disease. This variant is not observed in version 2.1.1 of the Genome Aggregation Database. Functional studies) conducted in cell lines derived from patient fibroblasts demonstrated that this variant results in decreased expression of MRPL39 proteins which was corrected using lentiviral-mediated expression of wild-type MRPL39 (PMID: 37133451).Based on the available evidence, the c.896G>T p.(Gly299Val) variant is classified as likely pathogenic for primary mitochondrial disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024